Observations on Pluteaceae in Vietnam: Four New Species and New Records of Pluteus

Eighteen specimens of Pluteus collected from the tropical forests of Vietnam were studied using morphological and molecular approaches. Pluteus podospilloides, P. semibulbosus, P. chrysaegis and P. septocystidiatus are registered as additional or new records for Vietnam. Four species (P. conformis, P. lucidus, P. subroseus, and P. ornatus) are proposed as new to science, and several other collections (Pluteus sp. 1, P. aff. septocystidiatus, P. aff. pauperculus and P. cf. velutinus) are given an inconclusive taxonomic status for now. The taxonomic positions of all specimens were confirmed using DNA data (nrITS and tef1). Descriptions of the macro- and microscopic features of the studied collections with a discussion of similar taxa are given.

OP0222 IDENTIFICATION OF CAUSAL GENES AND MECHANISMS BY WHICH GENETIC VARIATION MEDIATES JUVENILE IDIOPATHIC ARTHRITIS SUSCEPTIBILITY USING FUNCTIONAL GENOMICS AND CRISPR-CAS9

Background

We recently performed the largest juvenile idiopathic arthritis (JIA) genome-wide association study (GWAS) to date 1. Disease-associated loci contain multiple single nucleotide polymorphism (SNPs), and the majority map to non-coding enhancers, making it challenging to define causal variants and genes.

Functional genomics datasets in disease-relevant tissues have shown to be essential for the functional interpretation of GWAS loci. In particular, capture Hi-C (CHi-C) has been successful in detecting chromosomal interactions linking GWAS loci to their target genes. However, such datasets are lacking in JIA.

Objectives

The aim of this study is to bridge this gap and advance the knowledge of the biological mechanisms that underpin susceptibility to JIA, by integrating GWAS with public epigenomics datasets and in-house generated CHi-C from JIA patients. We focus on CD4+ T-cells, which have been shown to be one of the most relevant cell types in JIA. In addition, we use CRISPR-Cas9 to validate the regulatory effect of prioritised variants on their predicted target genes.

Methods

Credible SNP sets for the top JIA risk loci (P < 5x10-6) were annotated using EpiMap data 2. Low input whole genome promoter CHi-C (PCHi-C) was performed on CD4+ T-cells isolated from blood from 3 JIA oligoarthritis patients, and data was analysed using CHiCAGO 3. GWAS and PCHi-C data were combined to prioritise causal genes using the Capture Hi-C Omnibus Gene Score (COGS) pipeline 4. We subsequently employed CRISPR activation (CRISPRa) and CRISPR interference (CRISPRi) in Jurkats to assess whether prioritized JIA variants were capable of regulating the expression of the interacting genes.

Results

614 credible SNPs (out of 735) were found to overlap active enhancers in CD4+ T-cells, and were prioritized for further analysis.

We identified numerous significant chromatin interactions in 19 out of 44 non-MHC JIA associated loci, linking JIA SNPs mapping to T-cell enhancers to a total of 61 target genes and revealing potential novel disease pathways. Moreover, COGS prioritised a total of 7 genes (RGS14, ERAP2, HIPK1, CCR4, CCRL2, CCR2, CCR3).

A JIA associated locus on chromosome 3 contains 39 SNPs. It maps to an intergenic region and the causal gene/s are unclear. Our PCHi-C data revealed that this JIA locus presents chromatin interactions with the promoters of several genes, such as CCRL2, CCR2, CCR3 and CCR5, three of which were prioritised by COGS. Two variants were selected for further analysis: rs79815064, which had the highest posterior probability, and rs8005404,the only variant within a CD4+ T-cell enhancer linked to surrounding gene activity.

When both SNPs were targeted with CRISPRa and CRISPRi, we observed an increased and decreased expression, respectively, of CCRL2, CCR2, CCR3 and CCR5, confirming their role in disease. These genes belong to the chemokine receptor family and are important regulators of the inflammatory response.

Conclusion

Our work shows how functional genomics can help identify biological mechanisms by which GWAS variants increase risk of JIA, which in turn will benefit patients through personalised medicine and the identification of therapeutic targets.

References

[1]López-Isac, E. et al. Combined genetic analysis of juvenile idiopathic arthritis clinical subtypes identifies novel risk loci, target genes and key regulatory mechanisms. Ann. Rheum. Dis.80, 321–328 (2021).

[2]Boix, C. A., James, B. T., Park, Y. P., Meuleman, W. & Kellis, M. Regulatory genomic circuitry of human disease loci by integrative epigenomics. Nat. 2021 5907845590, 300–307 (2021).

[3]Cairns, J. et al. CHiCAGO: Robust detection of DNA looping interactions in Capture Hi-C data. Genome Biol.17, 1–17 (2016).

[4]Javierre, B. M. et al. Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters. Cell167, 1369 (2016).

Disclosure of Interests

Antonio Frantzesko: None declared, Valeriya Malysheva: None declared, Chenfu Shi: None declared, James Ding: None declared, John Bowes: None declared, Wendy Thomson: None declared, Stephen Eyre: None declared, Mikhail Spivakov Shareholder of: co-founder and shareholder of Enhanc3D Genomics Ltd, Gisela Orozco: None declared

Revision of Cerinomyces (Dacrymycetes, Basidiomycota) with notes on morphologically and historically related taxa

Cerinomyces (Dacrymycetes, Basidiomycota) is a genus traditionally defined by corticioid basidiocarps, in contrast to the rest of the class, which is characterized by gelatinous ones. In the traditional circumscription the genus is polyphyletic, and the monotypic family Cerinomycetaceae is paraphyletic. Aiming for a more concise delimitation, we revise Cerinomyces s.l. with a novel phylogeny based on sequences of nrDNA (SSU, ITS, LSU) and protein-coding genes (RPB1, RPB2, TEF1-α). We establish that monophyletic Cerinomyces s.s. is best characterized not by the corticioid morphology, but by a combination of traits: hyphal clamps, predominantly aseptate thin-walled basidiospores, and low content of carotenoid pigments. In our updated definition, Cerinomyces s.s. encompasses five well-supported phylogenetic clades divided into two morphological groups: (i-iii) taxa with arid corticioid basidiocarps, including the generic type C. pallidus; and (iv-v) newly introduced members with gelatinous basidiocarps, like Dacrymyces enatus and D. tortus. The remaining corticioid species of Cerinomyces s.l. are morphologically distinct and belong to the Dacrymycetaceae: our analysis places the carotenoid-rich Cerinomyces canadensis close to Femsjonia, and we transfer the clamps-lacking C. grandinioides group to Dacrymyces. In addition, we address genera related to Cerinomyces s.l. historically and morphologically, such as Ceracea, Dacryonaema and Unilacryma. Overall, we describe twenty-four new species and propose nine new combinations in both Cerinomycetaceae and Dacrymycetaceae.

Fungal Planet description sheets: 951-1041

Novel species of fungi described in this study include those from various countries as follows: Antarctica, Apenidiella antarctica from permafrost, Cladosporium fildesense from an unidentified marine sponge. Argentina, Geastrum wrightii on humus in mixed forest. Australia, Golovinomyces glandulariae on Glandularia aristigera, Neoanungitea eucalyptorum on leaves of Eucalyptus grandis, Teratosphaeria corymbiicola on leaves of Corymbia ficifolia, Xylaria eucalypti on leaves of Eucalyptus radiata. Brazil, Bovista psammophila on soil, Fusarium awaxy on rotten stalks of Zea mays, Geastrum lanuginosum on leaf litter covered soil, Hermetothecium mikaniae-micranthae (incl. Hermetothecium gen. nov.) on Mikania micrantha, Penicillium reconvexovelosoi in soil, Stagonosporopsis vannaccii from pod of Glycine max. British Virgin Isles, Lactifluus guanensis on soil. Canada, Sorocybe oblongispora on resin of Picea rubens. Chile, Colletotrichum roseum on leaves of Lapageria rosea. China, Setophoma caverna from carbonatite in Karst cave. Colombia, Lareunionomyces eucalypticola on leaves of Eucalyptus grandis. Costa Rica, Psathyrella pivae on wood. Cyprus, Clavulina iris on calcareous substrate. France, Chromosera ambigua and Clavulina iris var. occidentalis on soil. French West Indies, Helminthosphaeria hispidissima on dead wood. Guatemala, Talaromyces guatemalensis in soil. Malaysia, Neotracylla pini (incl. Tracyllales ord. nov. and Neotracylla gen. nov.) and Vermiculariopsiella pini on needles of Pinus tecunumanii. New Zealand, Neoconiothyrium viticola on stems of Vitis vinifera, Parafenestella pittospori on Pittosporum tenuifolium, Pilidium novae-zelandiae on Phoenix sp. Pakistan, Russula quercus-floribundae on forest floor. Portugal, Trichoderma aestuarinum from saline water. Russia, Pluteus liliputianus on fallen branch of deciduous tree, Pluteus spurius on decaying deciduous wood or soil. South Africa, Alloconiothyrium encephalarti, Phyllosticta encephalarticola and Neothyrostroma encephalarti (incl. Neothyrostroma gen. nov.) on leaves of Encephalartos sp., Chalara eucalypticola on leaf spots of Eucalyptus grandis × urophylla, Clypeosphaeria oleae on leaves of Olea capensis, Cylindrocladiella postalofficium on leaf litter of Sideroxylon inerme, Cylindromonium eugeniicola (incl. Cylindromonium gen. nov.) on leaf litter of Eugenia capensis, Cyphellophora goniomatis on leaves of Gonioma kamassi, Nothodactylaria nephrolepidis (incl. Nothodactylaria gen. nov. and Nothodactylariaceae fam. nov.) on leaves of Nephrolepis exaltata, Falcocladium eucalypti and Gyrothrix eucalypti on leaves of Eucalyptus sp., Gyrothrix oleae on leaves of Olea capensis subsp. macrocarpa, Harzia metrosideri on leaf litter of Metrosideros sp., Hippopotamyces phragmitis (incl. Hippopotamyces gen. nov.) on leaves of Phragmites australis, Lectera philenopterae on Philenoptera violacea, Leptosillia mayteni on leaves of Maytenus heterophylla, Lithohypha aloicola and Neoplatysporoides aloes on leaves of Aloe sp., Millesimomyces rhoicissi (incl. Millesimomyces gen. nov.) on leaves of Rhoicissus digitata, Neodevriesia strelitziicola on leaf litter of Strelitzia nicolai, Neokirramyces syzygii (incl. Neokirramyces gen. nov.) on leaf spots of Syzygium sp., Nothoramichloridium perseae (incl. Nothoramichloridium gen. nov. and Anungitiomycetaceae fam. nov.) on leaves of Persea americana, Paramycosphaerella watsoniae on leaf spots of Watsonia sp., Penicillium cuddlyae from dog food, Podocarpomyces knysnanus (incl. Podocarpomyces gen. nov.) on leaves of Podocarpus falcatus, Pseudocercospora heteropyxidicola on leaf spots of Heteropyxis natalensis, Pseudopenidiella podocarpi, Scolecobasidium podocarpi and Ceramothyrium podocarpicola on leaves of Podocarpus latifolius, Scolecobasidium blechni on leaves of Blechnum capense, Stomiopeltis syzygii on leaves of Syzygium chordatum, Strelitziomyces knysnanus (incl. Strelitziomyces gen. nov.) on leaves of Strelitzia alba, Talaromyces clemensii from rotting wood in goldmine, Verrucocladosporium visseri on Carpobrotus edulis. Spain, Boletopsis mediterraneensis on soil, Calycina cortegadensisi on a living twig of Castanea sativa, Emmonsiellopsis tuberculata in fluvial sediments, Mollisia cortegadensis on dead attached twig of Quercus robur, Psathyrella ovispora on soil, Pseudobeltrania lauri on leaf litter of Laurus azorica, Terfezia dunensis in soil, Tuber lucentum in soil, Venturia submersa on submerged plant debris. Thailand, Cordyceps jakajanicola on cicada nymph, Cordyceps kuiburiensis on spider, Distoseptispora caricis on leaves of Carex sp., Ophiocordyceps khonkaenensis on cicada nymph. USA, Cytosporella juncicola and Davidiellomyces juncicola on culms of Juncus effusus, Monochaetia massachusettsianum from air sample, Neohelicomyces melaleucae and Periconia neobrittanica on leaves of Melaleuca styphelioides × lanceolata, Pseudocamarosporium eucalypti on leaves of Eucalyptus sp., Pseudogymnoascus lindneri from sediment in a mine, Pseudogymnoascus turneri from sediment in a railroad tunnel, Pulchroboletus sclerotiorum on soil, Zygosporium pseudomasonii on leaf of Serenoa repens. Vietnam, Boletus candidissimus and Veloporphyrellus vulpinus on soil. Morphological and culture characteristics are supported by DNA barcodes.

A preliminary overview of the corticioid Atractiellomycetes (Pucciniomycotina, Basidiomycetes)

The taxonomy of the corticioid fungi from the class Atractiellomycetes (Pucciniomycotina, Basidiomycetes) currently addressed to the genus Helicogloea, is revised based on morphological and nuclear ribosomal DNA (ITS and LSU) data. The genus is restricted to 25 species with semitranslucent, gelatinous basidiocarps lacking differentiated cystidia and clamps on hyphae, of which 11 are described as new to science. The asexual genus Leucogloea is placed as a synonym of Helicogloea s. str. Since the type species of Saccoblastia, S. ovispora, is combined to Helicogloea, a new genus, Saccosoma, is introduced to encompass Saccoblastia farinacea and six related species, one of which is described as new. In contrast to Helicogloea in the strict sense, the basidiocarps of Saccosoma are arid, not gelatinized, and hyphae are clamped. The third lineage of the corticioid Atractiellomycetes is represented by the Bourdotigloea vestita complex. Species of Bourdotigloea are devoid of clamps but often possess well-differentiated cystidia, as well as long, cylindrical-fusiform basidiospores. Bourdotigloea encompasses nine species, of which six are described here as new.

Considerations and consequences of allowing DNA sequence data as types of fungal taxa

Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.